Palynological analysis was carried out on 135 samples of Greek thyme honeys, selected from three experimental apiaries under controlled conditions. Samples of all plants in flower growing around the bee colonies were collected and a comparison of their pollen was made with pollen grains identified in the honeys. Pollen grains of Thymus capitatus were found in all honey samples with a content ranging from 27 to 95%, thus upgrading the designation of the Greek floral honey as thyme honey. A qualitative analysis revealed the presence in the honeys of pollen grains of 37 taxa belonging to 15 families. A quantitative analysis showed that the total number of pollen grains (NPG) in the honey samples had a considerable variation between areas with a mean value of 65,000 per 10 g of honey. As it appears to be influenced by many different factors, quantitative analysis cannot be used alone to identify the geographic origin of the honey. The geographical determination among the three studied areas was made possible by using unique pollen grain combinations of the plants growing in the area of production. A matrix representing the pollen grain frequencies of the species found in each honey sample was analyzed by means of a classification tree. A model of high predictive power was built on the basis of the pollen grain frequencies of only two species. Additionally, surrogate species of high predictive power were revealed from the analysis.